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Protein

Nuclear RNA export factor 1

Gene

NXF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in the nuclear export of mRNA species bearing retroviral constitutive transport elements (CTE) and in the export of mRNA from the nucleus to the cytoplasm (TAP/NFX1 pathway) (PubMed:10924507). The NXF1-NXT1 heterodimer is involved in the export of HSP70 mRNA in conjunction with ALYREF/THOC4 and THOC5 components of the TREX complex (PubMed:18364396, PubMed:19165146, PubMed:9660949). ALYREF/THOC4-bound mRNA is thought to be transferred to the NXF1-NXT1 heterodimer for export (PubMed:18364396, PubMed:19165146, PubMed:9660949). Also involved in nuclear export of m6A-containing mRNAs: interaction between SRSF3 and YTHDC1 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (PubMed:28984244).5 Publications

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processHost-virus interaction, mRNA transport, Transport

Enzyme and pathway databases

ReactomeiR-HSA-159227 Transport of the SLBP independent Mature mRNA
R-HSA-159230 Transport of the SLBP Dependant Mature mRNA
R-HSA-159231 Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
SIGNORiQ9UBU9

Protein family/group databases

TCDBi3.A.18.1.1 the nuclear mrna exporter (mrna-e) family

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear RNA export factor 1
Alternative name(s):
Tip-associated protein
Tip-associating protein
mRNA export factor TAP
Gene namesi
Name:NXF1
Synonyms:TAP
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000162231.13
HGNCiHGNC:8071 NXF1
MIMi602647 gene
neXtProtiNX_Q9UBU9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi71R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-78, A-81, A-82, A-89, A-91, A-97, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi78R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-81, A-82, A-89, A-91, A-97, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi81R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-82, A-89, A-91, A-97, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi82R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-89, A-91, A-97, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi89R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-82, A-91, A-97, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi91R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-82, A-89, A-97, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi97R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-82, A-89, A-91, A-98, A-100 and A-105. 1 Publication1
Mutagenesisi98R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-82, A-89, A-91, A-97, A-100 and A-105. 1 Publication1
Mutagenesisi100R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-82, A-89, A-91, A-97, A-98 and A-105. 1 Publication1
Mutagenesisi105R → A: Greatly reduces RNA binding and no effect on interaction with ALYREF/THOC4; when associated with A-71, A-78, A-81, A-82, A-89, A-91, A-97, A-98 and A-100. 1 Publication1
Mutagenesisi306 – 308ERE → AAA: Decreases the export of mRNAs from the nucleus. 3
Mutagenesisi383L → R: Diminishes nuclear rim staining and 80% reduction in mRNA export activity; when associated with R-386. Complete loss of nuclear rim staining and mRNA export activity; when associated with R-386 and A-594. 1 Publication1
Mutagenesisi386L → R: Diminishes nuclear rim staining and 80% reduction in mRNA export activity; when associated with R-383. Complete loss of nuclear rim staining and mRNA export activity; when associated with R-383 and A-594. 1 Publication1
Mutagenesisi399D → A: 60% reduction in mRNA export activity. 1 Publication1
Mutagenesisi450 – 453LRFR → AAAA: Abolishes interaction with THOC5 and CHTOP. 1 Publication4
Mutagenesisi453R → A: Impairs intramolecular interaction between RBD and NTF2. 1 Publication1
Mutagenesisi456 – 459KHTR → AAAA: Abolishes interaction with THOC5 and CHTOP, no effect on interaction with NXT1; enhances intramolecular interaction between RBD and NTF2, reduces RNA binding and mRNA export. 2 Publications4
Mutagenesisi456K → D: Impairs intramolecular interaction between RBD and NTF2; when associated with D-459. 1
Mutagenesisi459R → D: Impairs intramolecular interaction between RBD and NTF2; when associated with D-456. 1
Mutagenesisi482D → R: 90% reduction in mRNA export activity. 1 Publication1
Mutagenesisi518I → R: 98% reduction in mRNA export activity. 1 Publication1
Mutagenesisi521P → Q: 35% reduction in mRNA export activity. 1 Publication1
Mutagenesisi594W → A: Suppresses FG-nucleoporin binding. Diminishes nuclear rim staining and 88% reduction in mRNA export activity. Complete loss of nuclear rim staining and mRNA export activity; when associated with R-383 and R-386. 1 Publication1
Mutagenesisi595D → R: Suppresses FG-nucleoporin binding. 1
Mutagenesisi617F → A: Suppresses FG-nucleoporin binding. 1 Publication1

Organism-specific databases

DisGeNETi10482
OpenTargetsiENSG00000162231
PharmGKBiPA31858

Polymorphism and mutation databases

BioMutaiNXF1
DMDMi20139282

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002205292 – 619Nuclear RNA export factor 1Add BLAST618

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei9PhosphoserineCombined sources1
Modified residuei42Asymmetric dimethylarginine; alternateBy similarity1
Modified residuei42Omega-N-methylarginine; alternateBy similarity1
Modified residuei126Nitrated tyrosineBy similarity1

Keywords - PTMi

Acetylation, Methylation, Nitration, Phosphoprotein

Proteomic databases

EPDiQ9UBU9
PaxDbiQ9UBU9
PeptideAtlasiQ9UBU9
PRIDEiQ9UBU9
ProteomicsDBi84075
84076 [Q9UBU9-2]

PTM databases

iPTMnetiQ9UBU9
PhosphoSitePlusiQ9UBU9

Expressioni

Tissue specificityi

Expressed ubiquitously.

Gene expression databases

BgeeiENSG00000162231
CleanExiHS_NXF1
ExpressionAtlasiQ9UBU9 baseline and differential
GenevisibleiQ9UBU9 HS

Organism-specific databases

HPAiCAB016327
HPA061593

Interactioni

Subunit structurei

Heterodimer (via NTF2 domain) with NXT1 (PubMed:11583626). The formation of NXF1-NXT1 heterodimers is required for the NXF1-mediated nuclear mRNA export (PubMed:11583626). Forms a complex with RANBP2/NUP358, NXT1 and RANGAP1 (PubMed:14729961). Associates with the exon junction complex (EJC) and with the transcription/export (TREX) complex (PubMed:11707413, PubMed:22893130). Found in a mRNA complex with UPF3A and UPF3B (PubMed:11546873). Found in a post-splicing complex with RBM8A, UPF1, UPF2, UPF3A, UPF3B and RNPS1 (PubMed:11546874). Interacts (via N-terminus) with DHX9 (via N-terminus); this interaction is direct and negatively regulates NXF1-mediated nuclear export of constitutive transport element (CTE)-containing cellular mRNAs (PubMed:10924507). Interacts with ALYREF/THOC4 (PubMed:11707413, PubMed:14730019, PubMed:19165146, PubMed:23299939). Interacts with FYTTD1/UIF (PubMed:19836239). Interacts with EIF4A3 (PubMed:14730019). Interacts with NUPL2 (PubMed:10228171). Interacts with THOC5 (PubMed:19165146, PubMed:23299939). Interacts with CHTOP (PubMed:23299939, PubMed:23826332). Interacts with FRG1 (via N-terminus) (PubMed:21699900). Interacts with LUZP4 (PubMed:25662211). Interacts with FMR1; the interaction occurs in a mRNA-dependent and polyribosomes-independent manner in the nucleus (PubMed:18936162). Interacts with CPSF6 (via N-terminus); this interaction is direct (PubMed:19864460). Interacts with RBM15 (PubMed:17001072). Interacts with RBM15B (PubMed:19586903).22 Publications
(Microbial infection) Interacts with Saimiriine herpesvirus 2 TIP protein.1 Publication
(Microbial infection) Interacts with human herpes virus 1 (HHV-1) ICP27 protein; this interaction allows efficient export of HHV-1 early and late transcripts.1 Publication

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi115745, 1132 interactors
CORUMiQ9UBU9
DIPiDIP-31789N
IntActiQ9UBU9, 105 interactors
MINTiQ9UBU9
STRINGi9606.ENSP00000294172

Structurei

Secondary structure

1619
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi120 – 124Combined sources5
Helixi127 – 129Combined sources3
Helixi132 – 141Combined sources10
Beta strandi143 – 145Combined sources3
Beta strandi150 – 155Combined sources6
Beta strandi158 – 164Combined sources7
Helixi166 – 174Combined sources9
Turni176 – 178Combined sources3
Beta strandi190 – 193Combined sources4
Helixi198 – 201Combined sources4
Helixi206 – 218Combined sources13
Turni222 – 225Combined sources4
Beta strandi226 – 228Combined sources3
Helixi232 – 234Combined sources3
Helixi236 – 240Combined sources5
Helixi250 – 263Combined sources14
Beta strandi269 – 271Combined sources3
Helixi281 – 285Combined sources5
Helixi286 – 289Combined sources4
Beta strandi295 – 297Combined sources3
Helixi306 – 312Combined sources7
Beta strandi318 – 321Combined sources4
Helixi328 – 330Combined sources3
Helixi334 – 344Combined sources11
Beta strandi350 – 353Combined sources4
Helixi381 – 398Combined sources18
Helixi403 – 408Combined sources6
Beta strandi410 – 419Combined sources10
Helixi433 – 436Combined sources4
Turni442 – 444Combined sources3
Helixi448 – 454Combined sources7
Beta strandi455 – 458Combined sources4
Helixi459 – 466Combined sources8
Beta strandi472 – 474Combined sources3
Helixi476 – 478Combined sources3
Beta strandi480 – 486Combined sources7
Beta strandi491 – 501Combined sources11
Turni505 – 508Combined sources4
Beta strandi510 – 521Combined sources12
Beta strandi525 – 538Combined sources14
Helixi541 – 548Combined sources8
Beta strandi553 – 557Combined sources5
Helixi565 – 578Combined sources14
Helixi582 – 591Combined sources10
Turni592 – 594Combined sources3
Helixi596 – 608Combined sources13
Helixi614 – 617Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FO1X-ray2.90A/B102-372[»]
1FT8X-ray3.15A/B/C/D/E102-372[»]
1GO5NMR-A551-619[»]
1JKGX-ray1.90B371-619[»]
1JN5X-ray2.80B371-619[»]
1KOHX-ray3.80A/B/C/D96-372[»]
1KOOX-ray3.80A/B/C/D96-372[»]
1OAIX-ray1.00A561-619[»]
2Z5KX-ray2.60B53-82[»]
2Z5MX-ray3.00B53-82[»]
3RW6X-ray2.30A/B96-362[»]
3RW7X-ray3.00A/B/C/D96-362[»]
4WYKX-ray3.40A/C96-555[»]
ProteinModelPortaliQ9UBU9
SMRiQ9UBU9
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UBU9

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini119 – 198RRMAdd BLAST80
Repeati266 – 291LRR 1Add BLAST26
Repeati292 – 315LRR 2Add BLAST24
Repeati316 – 343LRR 3Add BLAST28
Repeati344 – 371LRR 4Add BLAST28
Domaini386 – 536NTF2PROSITE-ProRule annotationAdd BLAST151
Domaini565 – 619TAP-CPROSITE-ProRule annotationAdd BLAST55

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 198Interaction with ALYREF/THOC4 and LUZP41 PublicationAdd BLAST197
Regioni2 – 118RNA-binding (RBD)Add BLAST117
Regioni2 – 60Minor non-specific RNA-bindingAdd BLAST59
Regioni61 – 118Major non-specific RNA-bindingAdd BLAST58

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi67 – 100Nuclear localization signalAdd BLAST34
Motifi83 – 110Nuclear export signalAdd BLAST28

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi551 – 561Pro-richAdd BLAST11

Domaini

The minimal CTE binding domain consists of an RNP-type RNA binding domain (RBD) and leucine-rich repeats.1 Publication
The nucleoporin binding domain consists of a NTF2 domain (also called NTF2-like domain) and a TAP-C domain (also called UBA-like domain). It has 2 nucleoporin-FG-repeats binding sites (one in the NTF2 and the other in the TAP-C domain) which contribute to nucleoporin association and act synergistically to export cellular mRNAs.1 Publication
The NTF2 domain is functional only in the presence of NXT1 and is essential for the export of mRNA from the nucleus. It inhibits RNA binding activity through an intramolecular interaction with the N-terminal RNA binding domain (RBD); the inhibition is removed by an association with the TREX complex, specifically involving ALYREF/THOC4 and THOC5.1 Publication
The TAP-C domain mediates direct interactions with nucleoporin-FG-repeats and is necessary and sufficient for localization of NXF1 to the nuclear rim. The conserved loop 594-NWD-596 of the TAP-C domain has a critical role in the interaction with nucleoporins.1 Publication
The leucine-rich repeats are essential for the export of mRNA from the nucleus.1 Publication
The RNA-binding domain is a non-canonical RNP-type domain.1 Publication

Sequence similaritiesi

Belongs to the NXF family.Curated

Keywords - Domaini

Leucine-rich repeat, Repeat

Phylogenomic databases

eggNOGiKOG3763 Eukaryota
ENOG410XR55 LUCA
GeneTreeiENSGT00390000007539
HOGENOMiHOG000236269
HOVERGENiHBG013199
InParanoidiQ9UBU9
KOiK14284
OMAiSYFGTET
OrthoDBiEOG091G04QA
PhylomeDBiQ9UBU9
TreeFamiTF314566

Family and domain databases

CDDicd00780 NTF2, 1 hit
cd14342 UBA_TAP-C, 1 hit
Gene3Di3.30.70.330, 1 hit
3.80.10.10, 1 hit
InterProiView protein in InterPro
IPR001611 Leu-rich_rpt
IPR032675 LRR_dom_sf
IPR002075 NTF2
IPR032710 NTF2-like_dom_sf
IPR018222 Nuclear_transport_factor_2_euk
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR030217 NXF_fam
IPR035979 RBD_domain_sf
IPR005637 TAP_C_dom
IPR015245 Tap_RNA-bd
IPR009060 UBA-like_sf
PANTHERiPTHR10662 PTHR10662, 1 hit
PfamiView protein in Pfam
PF02136 NTF2, 1 hit
PF09162 Tap-RNA_bind, 1 hit
PF03943 TAP_C, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD043466 Tap_RNA_bd, 1 hit
SMARTiView protein in SMART
SM00804 TAP_C, 1 hit
SUPFAMiSSF46934 SSF46934, 1 hit
SSF54427 SSF54427, 1 hit
SSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS51450 LRR, 3 hits
PS50177 NTF2_DOMAIN, 1 hit
PS51281 TAP_C, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UBU9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MADEGKSYSE HDDERVNFPQ RKKKGRGPFR WKYGEGNRRS GRGGSGIRSS
60 70 80 90 100
RLEEDDGDVA MSDAQDGPRV RYNPYTTRPN RRGDTWHDRD RIHVTVRRDR
110 120 130 140 150
APPERGGAGT SQDGTSKNWF KITIPYGRKY DKAWLLSMIQ SKCSVPFTPI
160 170 180 190 200
EFHYENTRAQ FFVEDASTAS ALKAVNYKIL DRENRRISII INSSAPPHTI
210 220 230 240 250
LNELKPEQVE QLKLIMSKRY DGSQQALDLK GLRSDPDLVA QNIDVVLNRR
260 270 280 290 300
SCMAATLRII EENIPELLSL NLSNNRLYRL DDMSSIVQKA PNLKILNLSG
310 320 330 340 350
NELKSERELD KIKGLKLEEL WLDGNSLCDT FRDQSTYISA IRERFPKLLR
360 370 380 390 400
LDGHELPPPI AFDVEAPTTL PPCKGSYFGT ENLKSLVLHF LQQYYAIYDS
410 420 430 440 450
GDRQGLLDAY HDGACCSLSI PFIPQNPARS SLAEYFKDSR NVKKLKDPTL
460 470 480 490 500
RFRLLKHTRL NVVAFLNELP KTQHDVNSFV VDISAQTSTL LCFSVNGVFK
510 520 530 540 550
EVDGKSRDSL RAFTRTFIAV PASNSGLCIV NDELFVRNAS SEEIQRAFAM
560 570 580 590 600
PAPTPSSSPV PTLSPEQQEM LQAFSTQSGM NLEWSQKCLQ DNNWDYTRSA
610
QAFTHLKAKG EIPEVAFMK
Length:619
Mass (Da):70,182
Last modified:May 1, 2000 - v1
Checksum:i338872AADA789FBF
GO
Isoform 2 (identifier: Q9UBU9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     339-356: SAIRERFPKLLRLDGHEL → RSVVACVSPPGDLHPLGG
     357-619: Missing.

Show »
Length:356
Mass (Da):40,476
Checksum:i470701F5324EC0B5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti119W → C in AAB81111 (PubMed:9175835).Curated1
Sequence conflicti256T → N in AAD20016 (PubMed:10454577).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_041427339 – 356SAIRE…DGHEL → RSVVACVSPPGDLHPLGG in isoform 2. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_041428357 – 619Missing in isoform 2. 1 PublicationAdd BLAST263

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ132712 mRNA Translation: CAA10753.1
AF112880 mRNA Translation: AAD39102.1
AF126246 mRNA Translation: AAD20016.1
AK304137 mRNA Translation: BAG65031.1
AK027192 mRNA No translation available.
AP001160 Genomic DNA No translation available.
CH471076 Genomic DNA Translation: EAW74105.1
BC004904 mRNA Translation: AAH04904.1
BC028041 mRNA Translation: AAH28041.1
U80073 mRNA Translation: AAB81111.1
CCDSiCCDS44629.1 [Q9UBU9-2]
CCDS8037.1 [Q9UBU9-1]
RefSeqiNP_001074960.1, NM_001081491.1 [Q9UBU9-2]
NP_006353.2, NM_006362.4 [Q9UBU9-1]
UniGeneiHs.523739
Hs.601546

Genome annotation databases

EnsembliENST00000294172; ENSP00000294172; ENSG00000162231 [Q9UBU9-1]
ENST00000531709; ENSP00000453885; ENSG00000162231 [Q9UBU9-2]
ENST00000532297; ENSP00000436679; ENSG00000162231 [Q9UBU9-1]
GeneIDi10482
KEGGihsa:10482
UCSCiuc001nvf.1 human [Q9UBU9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiNXF1_HUMAN
AccessioniPrimary (citable) accession number: Q9UBU9
Secondary accession number(s): B4E269, Q99799, Q9UQL2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: May 1, 2000
Last modified: June 20, 2018
This is version 202 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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